Analyzing Mosquito Data

Introduction

This material assumes that you have programmed before. This first lecture provides a quick introduction to programming in Python for those who either haven’t used Python before or need a quick refresher.

Let’s start with a hypothetical problem we want to solve. We are interested in understanding the relationship between the weather and the number of mosquitos occuring in a particular year so that we can plan mosquito control measures accordingly. Since we want to apply these mosquito control measures at a number of different sites we need to understand both the relationship at a particular site and whether or not it is consistent across sites. The data we have to address this problem comes from the local government and are stored in tables in comma-separated values (CSV) files. Each file holds the data for a single location, each row holds the information for a single year at that location, and the columns hold the data on both mosquito numbers and the average temperature and rainfall from the beginning of mosquito breeding season. The first few rows of our first file look like:

The read_csv() function belongs to the pandas library. In order to run it we need to tell Python that it is part of pandas and we do this using the dot notation, which is used everywhere in Python to refer to parts of larger things.

When we are finished typing and press Shift+Enter, the notebook runs our command and shows us its output. In this case, the output is the data we just loaded.

Our call to pandas.read_csv() read data into memory, but didn’t save it anywhere. To do that, we need to assign the array to a variable. In Python we use = to assign a new value to a variable like this:

data = pandas.read_csv('A1_mosquito_data.csv')

This statement doesn’t produce any output because assignment doesn’t display anything. If we want to check that our data has been loaded, we can print the variable’s value:

This tells the IPython Notebook to display the data object, which is why we see a pretty formated table.

Manipulating data

Once we have imported the data we can start doing things with it. First, let’s ask what type of thing data refers to:

printtype(data)

<class 'pandas.core.frame.DataFrame'>

The data is stored in a data structure called a DataFrame. There are other kinds of data structures that are also commonly used in scientific computing including Numpy arrays, and Numpy matrices, which can be used for doing linear algebra.

There are a couple of important things to note here. First, Python indexing starts at zero. In contrast, programming languages like R and MATLAB start counting at 1, because that’s what human beings have done for thousands of years. Languages in the C family (including C++, Java, Perl, and Python) count from 0 because that’s simpler for computers to do. This means that if we have 5 things in Python they are numbered 0, 1, 2, 3, 4, and the first row in a data frame is always row 0.

The other thing to note is that the subset of rows starts at the first value and goes up to, but does not include, the second value. Again, the up-to-but-not-including takes a bit of getting used to, but the rule is that the difference between the upper and lower bounds is the number of values in the slice.

One thing that we can’t do with this syntax is directly ask for the data from a single row:

That looks good, but why did we use 9.0 instead of 9? The reason is that computers store integers and numbers with decimals as different types: integers and floating point numbers (or floats). Addition, subtraction and multiplication work on both as we’d expect, but division works differently. If we divide one integer by another, we get the quotient without the remainder:

print'10/3 is:', 10 / 3

10/3 is: 3

If either part of the division is a float, on the other hand, the computer creates a floating-point answer:

print'10/3.0 is:', 10 / 3.0

10/3.0 is: 3.33333333333

The computer does this for historical reasons: integer operations were much faster on early machines, and this behavior is actually useful in a lot of situations. However, it’s still confusing, so Python 3 produces a floating-point answer when dividing integers if it needs to. We’re still using Python 2.7 in this class, so if we want 5/9 to give us the right answer, we have to write it as 5.0/9, 5/9.0, or some other variation.

Conditionals

The other standard thing we need to know how to do in Python is conditionals, or if/then/else statements. In Python the basic syntax is:

if condition:
do_something

So if we want to loop over the temperatures and print out only those temperatures that are greater than 80 degrees we would use:

Challenge

Import the data from A2_mosquito_data.csv, determine the mean temperate, and loop over the temperature values. For each value print out whether it is greater than the mean, less than the mean, or equal to the mean.

Plotting

The mathematician Richard Hamming once said, “The purpose of computing is insight, not numbers,” and the best way to develop insight is often to visualize data. The main plotting library in Python is matplotlib. To get started, let’s tell the IPython Notebook that we want our plots displayed inline, rather than in a separate viewing window:

%matplotlib inline

The % at the start of the line signals that this is a command for the notebook, rather than a statement in Python. Next, we will import the pyplot module from matplotlib, but since pyplot is a fairly long name to type repeatedly let’s give it an alias.

from matplotlib import pyplot as plt

This import statement shows two new things. First, we can import part of a library by using the from library import submodule syntax. Second, we can use a different name to refer to the imported library by using as newname.

Now, let’s make a simple plot showing how the number of mosquitos varies over time. We’ll use the site you’ve been doing exercises with since it has a longer time-series.

Challenge

Using the data in A2_mosquito_data.csv plot the relationship between the number of mosquitos and temperature and the number of mosquitos and rainfall.

Key Points

Import a library into a program using import libraryname.

Use the pandas library to work with data tables in Python.

Use variable = value to assign a value to a variable.

Use print something to display the value of something.

Use dataframe['columnname'] to select a column of data.

Use dataframe[start_row:stop_row] to select rows from a data frame.

Indices start at 0, not 1.

Use dataframe.mean(), dataframe.max(), and dataframe.min() to calculate simple statistics.

Use for x in list: to loop over values

Use if condition: to make conditional decisions

Use the pyplot library from matplotlib for creating simple visualizations.

Next steps

With the requisite Python background out of the way, now we’re ready to dig in to analyzing our data, and along the way learn how to write better code, more efficiently, that is more likely to be correct.